A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
/home/runner/work/pmultiqc/pmultiqc/data
pmultiqc
pmultiqc is a MultiQC module to show the pipeline performance of mass spectrometry based quantification pipelines such as nf-core/quantms, MaxQuant.URL: https://github.com/bigbio/pmultiqc
Experiment Setup
Parameters
| No. | Parameter | Value |
|---|---|---|
| 1 | Version | 1.5.2.8 |
| 2 | User name | cbielow |
| 3 | Machine name | CD02-WIN7 |
| 4 | Date of writing | 08/05/2015 11:38:59 |
| 5 | Fixed modifications | Carbamidomethyl (C) |
| 6 | Decoy mode | revert |
| 7 | Special AAs | KR |
| 8 | Include contaminants | True |
| 9 | MS/MS tol. (FTMS) | 20 ppm |
| 10 | Top MS/MS peaks per 100 Da. (FTMS) | 12 |
| 11 | MS/MS deisotoping (FTMS) | True |
| 12 | MS/MS tol. (ITMS) | 0.5 Da |
| 13 | Top MS/MS peaks per 100 Da. (ITMS) | 8 |
| 14 | MS/MS deisotoping (ITMS) | False |
| 15 | MS/MS tol. (TOF) | 40 ppm |
| 16 | Top MS/MS peaks per 100 Da. (TOF) | 10 |
| 17 | MS/MS deisotoping (TOF) | True |
| 18 | MS/MS tol. (Unknown) | 0.5 Da |
| 19 | Top MS/MS peaks per 100 Da. (Unknown) | 8 |
| 20 | MS/MS deisotoping (Unknown) | False |
| 21 | PSM FDR | 0.0 |
| 22 | Protein FDR | 0.0 |
| 23 | Site FDR | 0.0 |
| 24 | Use Normalized Ratios For Occupancy | True |
| 25 | Min. peptide Length | 7 |
| 26 | Min. score for unmodified peptides | 0 |
| 27 | Min. score for modified peptides | 40 |
| 28 | Min. delta score for unmodified peptides | 0 |
| 29 | Min. delta score for modified peptides | 6 |
| 30 | Min. unique peptides | 0 |
| 31 | Min. razor peptides | 1 |
| 32 | Min. peptides | 1 |
| 33 | Use only unmodified peptides and | True |
| 34 | Modifications included in protein quantification | Acetyl (Protein N-term);Oxidation (M) |
| 35 | Peptides used for protein quantification | Razor |
| 36 | Discard unmodified counterpart peptides | True |
| 37 | Min. ratio count | 2 |
| 38 | Re-quantify | False |
| 39 | Use delta score | False |
| 40 | iBAQ | False |
| 41 | iBAQ log fit | False |
| 42 | Match between runs | True |
| 43 | Matching time window [min] | 0.7 |
| 44 | Alignment time window [min] | 20 |
| 45 | Find dependent peptides | False |
| 46 | Fasta file | crap_withMycoplasma.fasta;uniprot_human_canonical_and_isoforms_20130513.fasta |
| 47 | Labeled amino acid filtering | True |
| 48 | Site tables | Oxidation (M)Sites.txt |
| 49 | RT shift | False |
| 50 | Advanced ratios | True |
| 51 | First pass AIF correlation | 0.8 |
Summary and HeatMap
Summary Table
| #MS2 Spectra | #Identified MS2 Spectra | %Identified MS2 Spectra | #Peptides Identified | #Proteins Identified | #Proteins Quantified |
|---|---|---|---|---|---|
| 201567 | 84900 | 42.12% | 28949 | 4053 | 4048 |